Generation of Molecular Surface

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Generation of Molecular Surface

Postby mwells » Mon Jun 30, 2014 3:59 pm

Hi Sargis - so I purchased PyRx 0.9 for home (Windows 8) and we have purchased it at University (linux environment). In both cases I can't generate the molecular surface and get this error message:

Traceback (most recent call last):
File "/home/hpc2854/.PyRx_workspace/update/PyRx/molNavigator.py", line 548, in OnDisplaySufrace
self.frame.mayaviEngine.DisplayMolecularSurface(molecule)
File "/home/hpc2854/.PyRx_workspace/update/PyRx/mayaviEngine.py", line 219, in DisplayMolecularSurface
img = tvtk.tvtk.tvtk.ImageData(origin=[origX,origY,origZ], spacing=[1,1,1], dimensions=[dimX, dimY, dimZ] )
AttributeError: 'module' object has no attribute 'tvtk'
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Re: Generation of Molecular Surface

Postby sargis » Tue Jul 01, 2014 1:37 am

Hi Mike - thank you for the message and sorry about that. I've uploaded new updates this fix this. Please use PyRx > Help > Check for Updates... menu and let me know if that fixes this.

Thank you for using PyRx!
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Re: Generation of Molecular Surface

Postby mwells » Tue Jul 01, 2014 1:43 pm

Hi Sargis - so it worked in Windows but not in Linux environment. However I am using PyRx via linux in a terminal server environment using web-based access. I will ask our IT tech if that is the issue and perhaps the updates are not truly "updating"

Cheers,

Mike
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Re: Generation of Molecular Surface

Postby mwells » Thu Jul 03, 2014 2:21 pm

Hi Sargis,

so the Linux update was applied without success - I still get this error:

Traceback (most recent call last):
File "/opt/PyRx/0.9.2/lib64/python2.6/site-packages/PyRx/molNavigator.py", line 548, in OnDisplaySufrace
self.frame.mayaviEngine.DisplayMolecularSurface(molecule)
File "/opt/PyRx/0.9.2/lib64/python2.6/site-packages/PyRx/mayaviEngine.py", line 219, in DisplayMolecularSurface
img = tvtk.tvtk.tvtk.ImageData(origin=[origX,origY,origZ], spacing=[1,1,1], dimensions=[dimX, dimY, dimZ] )
AttributeError: 'module' object has no attribute 'tvtk'
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Re: Generation of Molecular Surface

Postby sargis » Thu Jul 03, 2014 3:58 pm

Hi Mike,

Thank you much and sorry about this second problem with the update. I'll work on fixing this. In the meantime, please have a root user or someone with write access privileges to /opt/PyRx run the following command:

Code: Select all
cd /opt/PyRx/0.9.2/lib64/python2.6/site-packages/PyRx
svn update

Please let me know if this helps.

I appreciate your feedback and thank you for using PyRx!
Sargis
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Re: Generation of Molecular Surface

Postby mwells » Thu Jul 31, 2014 1:57 pm

Hello Sargis - the gentleman in charge of the program has provided me the following:

II am not quite sure what the command below means. I am guessing that I have to do this:

hasch@swlogin1$ cd /opt/PyRx/0.9.2/lib64/python2.6/site-packages/PyRx
hasch@swlogin1$ svn update
svn: Can't connect to host 'svn.code.sf.net': Connection refused

but something seems to be going wrong. This could have something to do with some current firewall issues which will soon be resolved. We will try again then.
Meanwhile, if possible, could you clarify with Sargis ? I don't know what to make of the "Code: Select all" part of the lines below.
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Re: Generation of Molecular Surface

Postby sargis » Thu Jul 31, 2014 3:26 pm

Hello Mike,

There is another method of doing updates. Visit http://sourceforge.net/p/pyrx/code/HEAD ... xDev/PyRx/ and click on Download Snapshot. Then unzip and overwrite files in/opt/PyRx/0.9.2/lib64/python2.6/site-packages/PyRx with the content of this zip file.
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